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Hi from Just Answer. I'm PDtax. I'll assist.
You will need to become an employee and set up withholding in NJ. You will also want to have NYC wage tax withheld regardless of being a NJ resident.
The s corp income (after wages) will be taxable to you in the state/city of operation, which will be NY and NYC. That income will be taxable on your personal NJ return, and subject to resident tax credits against your NJ income.
Since your S corp was in operation in 2015, you may need to file a short period return for the business. Best to review your operations, revenues/expenses with a tax pro who can advise if and how to file the short period return.
Hope that covers everything. Positive feedback is appreciated. I'm PDtax.